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Fixes #120, and also includes initial conditions for all models that use the model/end format. Also fixes a few typos, and syncs with some documentation apparently added to the Tellurium version of this documentation, but hadn't made it here. Translated versions now created with pandoc; the .md version is officially canonical.
Further fix for #120: include compartment size in rate rule.
These changes are to replace FluxBounds with reaction upper and lower bound attributes, and to allow quadratic objectives.
* Ensure constraints with integers get flagged as integers in SBML. * Only calculate flux bounds once. * Don't export FBC constraints as normal constraints, too.
Updates to make Antimony FBC Version 3 (and 2) compatible.
Since they are always amount, "S1=5" should set the initial amount, not the initial concentration. Similarly, "S1=5/C" and "S1=5*C" should be handled differently depending on whether the species is set substanceOnly or not.
Change how substanceOnly species are initialized.
Words like 'biological_system' were simply misleading too often. Just say what they actually are.
Change the default verbiage of annotation terms to match what they are.
* The new bqb terms are used. * New initial condition for substanceOnly species. * Some values are fixed that looked weird before (30.1.4?)
For some reason, the Windows parser sometimes chokes on Antimony files, but it can be fixed by adding a space to the end of the line before the line where it chokes. This adds those spaces so all the files can be read.
Update version number to 3.1.0
This first commit just turns things on again so that I can see what the problems are in the CI.
Update dependencies.
Fix storing individual segments in reaction arcs.
Don't require zip if there's no libsbml compression.
…les. For libantimonyjs, we need to define expat locations without CMake.
Provide a way to tell Antimony about expat without involving cmake files.
Wrap libsbml the same way.
Also switch to using macos15-intel instead of 13, since 13 is going away.
Fix unit bug; update version number.
A bugfix in that library now allows multi-segment reaction arcs in Antimony. Version and test updated.
Also add a bunch of literal unit tests (ha ha).
Units for substance-only species should be substance.
Update docs with full layout example.
Also, bump version number, and update some old docs.
Use updated libsbml to fix memory leak.
The libsbml fix ended up being slightly different than proposed; this uses the new form instead of the initially-proposed form.
Update for libsbml.
Github actions is complaining about node20; update stuff.
Handle reaction arc colors and line widths.
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